First Principle Study of the Terahertz and Far-Infrared Spectral Signatures in DNA Bonded to Silicon Nanodots

Abstract

The first principle study of hydrogen-terminated silicon (111) with deoxyguanosine (dG) residues chemically bonded to a silicon surface via Carbon linkers is performed to reveal new insights into the spectral signatures of constrained DNA chains. Silicon surface structure models are generated to accommodate one or two dG residues. In particular, structural models for two dG residues bonded onto silicon nanodots and that formed a single strand of DNA in the lateral direction (along the surface) were developed. First principle simulations with valence electron basis and effective core potentials are conducted. These studies utilized all-atom geometric optimizations to determine the final conformations and normal mode analyses to derive the spectral absorption information. Stable dG conformations on silicon are obtained for varying types of DNA chain length and Nanodot size/shape. These results show that optically active modes lying within the terahertz spectrum typically arise out of joint coupling between the DNA's vibrational behavior and that of the substrate. However, the dominant absorption line below 6 THz is predicted to most strongly represent the DNA dynamics and effects of sodium, but it is only weakly influenced by the Nanodot vibrations. In this study, the phonon-induced light absorption spectra of the DNA chains were analyzed in the context of nanodot influence (e.g., edge effects). These results suggest that DNA strands can be chemically bonded to arbitrary nanosized features on silicon surfaces without perturbing some of the key spectral signatures in the THz regime, and this suggests active THz illumination strategies for DNA identification and characterization.

Hybrid Ab Initio/Empirical Modeling of the Conformations and Light-Induced Transitions in Stilbene-Derivatives Bonded to DNA

“…Hence, the detectability of rather subtle structure changes by THz spectral fingerprinting is suggested because the adding/removing of the TMS end capping is predicted to strongly influence the collective motions of the entire molecule. At the same time, a detailed study of the entire absorption spectrum (i.e., but not presented here) reveals no significant changes at IR wavelengths, which is known to be a typical result [1] and the underlying motivation for the long wavelength studies presented here.…”

“…In particular, simulations on molecular conformation, dynamics and associated interactions (i.e., including far-IR and terahertz (THz) spectral absorption and emission) usually require the application of ab initio models. However, research into new nanotechnology concepts that seeks to identify novel functionality derived from nanoscale-dictated electronic, photonic, and/or phonon processes usually involves modeling and simulation of very large and complex bioorganic molecular systems [1]. Even a single biomolecule can consist of hundreds of thousands of atoms.…”

Advanced nanoelectronic architectures for THz-based biological agent detection

“…Preliminary theoretical results have already suggested much promise for this concept because: (i) one can expect to obtain robust absorption features across the THz-IR frequency spectrum that are linked to base-pair sequence structure [11]; and (ii) it is possible to identify absorption modes that are extremely insensitive to the surface contact morphology [12]. These general characteristics are illustrated in the results given in Fig.…”